The invention relates to a method for treatment of water, permitting the physico-chemical treatment of water, including a ballasted flocculation stage using a granular ballast material with a density greater than water, followed by, a stage of gravity separation of the treated water and the flocculent mass, a stage of separation of the granular material, recycled for the flocculation stage and the muds. Said muds are sent to a stage for treatment of the muds, characterised in comprising a stage in which the functional mode passes from a mode using ballasted flocculation and gravity separation using coagulation and flocculation reagents to a mode functioning by simple gravity separation, without using coagulation and flocculation reagents. The passage from one mode to another is determined using at least one item of information on the water obtained at any stage of the treatment thereof or before said treatment.